Libyan rebels gather on armoured vehicles outside Sirte, one of the last strongholds of the fugitive leader Muammar Gaddafi. Photograph: Ciro Fusco/ANSA

Rebels as well as pro-Gaddafi forces have perpetrated killings, torture and other abuses during the uprising against the Libyan regime, say human rights investigators.

The civil war that brought down Muammar Gaddafi has been marked by widespread atrocities on both sides, according to Amnesty International.

In one of the most comprehensive reports yet on the human cost of the six-month conflict, Amnesty offers harrowing testimony of the war crimes, killings of unarmed protesters and arbitrary detentions by Gaddafi's security forces. But it also lifts the lid on a catalogue of reprisal attacks that have gained less international attention during the revolution.

"Opposition fighters and supporters have abducted, arbitrarily detained, tortured and killed former members of the security forces, suspected Gaddafi loyalists, captured soldiers and foreign nationals wrongly suspected of being mercenaries fighting on behalf of Gaddafi forces," Amnesty says.

"No independent or credible investigations are known to have been carried out by the NTC [opposition National Transitional Council], nor effective measures taken to hold to account those responsible for these abuses."

The report says that in the first days of the uprising, groups of protesters killed captured soldiers and suspected mercenaries in al-Bayda, Derna and Benghazi. "Some were beaten to death, at least three were hanged, and others were shot dead after they had been captured or had surrendered," the report says.

Those who tried to distance themselves from Gaddafi's military apparatus were often shown no mercy, Amnesty's researchers found.

A former member of Libya's internal security agency, Ibrahim Khalifa al-Surmani, a father of six, was found dead on 10 May in the outskirts of Benghazi. "He had been shot in the head. His hands and feet were bound and a scarf was tightly tied around his neck. He was missing a piece of flesh from his right calf and marks on his trousers indicated that he had been kneeling. A bloodstained note bearing his name was found by the body; it read: '... a dog among Gaddafi's dogs has been eliminated'."

Amnesty also found more recent unlawful killings "perpetrated by organised groups who operate freely, openly and with impunity". Victims' families were generally unwilling to protest for fear of reprisals and to avoid the stigma of being labelled Gaddafi loyalists or "anti-revolutionary". In addition, opposition groups have detained hundreds of people in areas they control since the end of February, Amnesty says. These include people accused of "subverting the revolution," who say they were never shown an arrest warrant or any other document.

"In most cases, the manner of detention is better described as abduction rather than arrest," the report argues. "They were seized by groups of heavily-armed men, some of them masked, who did not identify themselves. They were then taken away in unmarked vehicles, usually pick-up trucks with anti-aircraft machine-guns mounted at the back."

It continues: "None of the detainees, whether Libyan or foreign civilians, or Libyan soldiers, have had access to a lawyer, been formally charged, or been given the opportunity to challenge their detention before a judicial authority."

Several detainees, including Libyan and foreign civilians, as well as captured soldiers, told Amnesty that they were tortured. Most commonly reported methods included beatings all over the body with objects such as belts, metal bars, sticks, rifle butts and rubber hoses (at times directly on exposed flesh); electric shocks; and threats – including rape.

The report states: "Victims are subjected to beatings and other abuses seemingly to extract confessions and to punish them for their alleged 'crimes'. In some cases, detainees are forced to sign or thumb-print statements under torture or duress without being allowed to read them. In fact, several detainees told Amnesty International that they were interrogated while blindfolded."

Amnesty was shown video footage of a group of rebels taunting captured soldiers at the al-Jalaa hospital in Benghazi, forcing them to repeat "I am a Gaddafi dog," and chew paper.

A detainee at the Saadoun secondary school detention centre in Misrata claimed he was often beaten with a metal bar or belt or given electric shocks. "It is very painful," the man was quoted as saying. "He wants me to confess that I have killed, raped and stolen; at least one of these crimes. When I say that I didn't do any of these things he tortures me more harshly."

Amnesty says NTC officials have shown willingness to take steps to improve prison conditions and avoid future abuses, but seemed reluctant to investigate and bring those responsible to justice.

The NTC sought to distance itself from the alleged violations. A spokeswoman for the NTC said: "The Amnesty report is overwhelmingly filled with the horrific abuses and killings by the Gaddafi regime. However, there are a small number of incidents involving those opposed to Gaddafi; the NTC strongly condemns any abuses perpetrated by either side."

She added: "The NTC is firmly committed to upholding human rights and the rule of law, both international and local. The violation of rights no longer has a place in Libya. The NTC is putting its efforts to bring any armed groups under official authorities and will fully investigate any incidents brought to our attention."

The findings are largely based on Amnesty's visit to Libya between 26 February and 28 May, including to the cities of al-Bayda, Ajdabiya, Brega, Benghazi, Misrata and Ras Lanouf. The report claims foreigners have been targeted by both sides, particularly individuals with dark skin. But the report adds: The report says people with dark skin were targeted by both sides, but "the allegations about the use of mercenaries proved to be largely unfounded".

The report chronicles in depth the atrocities committed by Gaddafi loyalists, including artillery, mortar and rocket attacks against residential areas and use of indiscriminate weapons such as anti-personnel mines and cluster bombs. Civilians not involved in the fighting were killed and extra-judicial executions carried out.

Amnesty found an extensive campaign of enforced disappearances of perceived opponents across the country, including journalists, writers, online activists and protesters. Thousands of Libyans were abducted from their homes, mosques and streets, or captured near the frontline, frequently with the use of violence. Among the disappeared were children as young as 12.